Identification of a candidate gene controlling semi-dwarfism in watermelon, Citrullus lanatus, using a combination of genetic linkage mapping and QTL-seq

Abstract

Dwarfism in crops is a useful breeding trait. In this study, we aimed to identify a candidate gene controlling semi-dwarfism in watermelon (Citrullus lanatus) using a combination of genetic mapping and quantitative trait loci (QTL)-seq. We evaluated phenotypes using an F2 and F2:3 population derived from a cross between a “Bush Sugar Baby” (BSB, semi-dwarf type) and a PCL-J1 (normal type) cultivar. Results indicated that a single recessive gene confers semi-dwarfism in BSB. We constructed a genetic map using 180 F2 plants and 336 single-nucleotide polymorphisms (SNPs), detected using genotyping-by-sequencing, and mapped the semi-dwarfism locus, sdw-1, between the SNP markers linked by 9.6 cM (0.99 Mb) on Chr. 9. QTL analysis pointed to the same genomic location for sdw-1 using single-marker analysis. Further, based on the QTL-seq, we identified a significant genomic region for sdw-1 that matched with the sdw-1-flanking region in the genetic linkage map. This 1-Mb region was narrowed down by mapping three SNP markers developed from the QTL-seq data. The sdw-1 locus was mapped to the 0.44-Mb genomic region, which harbored 13 genes. One of the 13 genes, ClCG09G018320 (ATP-binding cassette (ABC) transporter B family member 19), showed the SNPs in its coding sequence, and cleaved amplified APS markers developed from those SNPs co-segregated with sdw-1 in fine mapping using 620 F2 plants. Our results implied that a frameshift mutation in the ABC transporter gene and the resulting alteration in auxin transportation are the most likely to be responsible for semi-dwarfism in BSB.

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Acknowledgements

This work was supported by a Grant (710001-07-5) from the Vegetable Breeding Research Center through the Agriculture, Food and Rural Affairs Research Center Support Program of the Ministry of Agriculture, Food and Rural Affairs (MAFRA), Korea. This study was also supported by a Grant (Project No: PJ014846012020) from National Institute of Horticultural Herbal Sciences, Rural Development Administration.

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YC, SL, JP, and SK carried out plant material preparation and phenotype evaluation. YC, SL, and GP carried out DNA extraction; YC, SL, and GP, and YP performed the NGS data analysis, genetic mapping, and QTL-seq analysis; YC, SL, and YP wrote the manuscript.

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Correspondence to Younghoon Park.

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Figure S1 Genetic linkage maps based on an F2 population derived from a cross between “Bush Sugar Baby” and PCL-J1 using 336 single-nucleotide polymorphisms (SNPs) (PDF 1542 kb)

Figure S2 SNP-index plots between N-bulk (a), D-bulk (b), and the ∆(SNP-index (c) (PDF 1545 kb)

Figure S3 Gene sequence of ClCG09G018320 encoding the ABC B family 19 protein and sequence variants between BSB and PCL-J (PDF 107 kb)

Figure S4 Comparison of plant heights between the semi-dwarf type “Bush Sugar Baby” (BSB), the extreme dwarf type “Caupat-dw,” and F1 plants from a cross between BSB and “Caupat-dw” six weeks (the 17–20-true-leaf stage) after germination (JPG 99 kb)

Table S1 Data for comparison of genome annotation and collinearity between the “97103” genome assembly version 1 and the “Charleston Gray” genome assembly version 2 (XLSX 269 kb)

Table S2 Data for genes and SNPs/Indels located in the physical distance (1 Mbp) between the sdw-1-flanking SNPs (“Charleston Gray” genome assembly version 2) (XLSX 83 kb)

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Cho, Y., Lee, S., Park, J. et al. Identification of a candidate gene controlling semi-dwarfism in watermelon, Citrullus lanatus, using a combination of genetic linkage mapping and QTL-seq. Hortic. Environ. Biotechnol. (2021). https://doi.org/10.1007/s13580-020-00330-x

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Keywords

  • ABC transporter
  • Citrullus lanatus
  • Genotyping-by-sequence
  • QTL-seq
  • Semi-dwarfism
  • Watermelon